Molecular modeling, docking and dynamics studies of fenugreek (Trigonella foenum-graecum) α-amylase

Abstract

α-Amylase catalyses the hydrolysis of glucosidic bonds in polysaccharides such as starch, glycogen and their degradation products. In the present study, the three-dimensional structure of fenugreek (Trigonella foenum-graecum) α-amylase was determined using a homology modeling-based technique. The best predicted model was deposited in PMDB server with PMDB ID PM0084364. The phylogenetic tree was created using the UPGMA method with 8 homologous protein sequences, Trigonella foenum-graecum was utilized as the target protein. Alignment of the phylogenetic tree identified two primary functional groupings (A and B). α-Amylase from the target genome Trigonella foenum-graecum (Acc. No: GHNA01022531.1) was clustered with Medicago truncatula (Acc. No: XP003589186.1), Cicer arietinum (Acc. No: XP004499059.1), Cajanus cajan (Acc. No: XP020231823.1), Vigna angularis (Acc. No: NP001316768.1) and Vigna mungo (Acc. No: P17859.1), in group A cluster, while Hordeum vulgare (Acc. No: Q40015) and Oryza sativa (PDB ID: 3WN6) were in cluster B. The molecular dynamics simulations were performed to understand the molecular basis and mode of action of Trigonella foenum-graecum α-amylase. Additionally, a geometry-based molecular docking technique was used to evaluate potential binding interactions between the modeled structure of α-amylase and maltose. The results show that Trp²²⁸, Glu²²⁶, Arg¹⁹⁹, His³⁰⁸, Tyr¹⁶⁵, Asp³⁰⁹, Phe²⁰² and Asp²⁰¹ from Trigonella foenum-graecum α-amylase enzyme is involved in the binding to the substrate maltose. Our study provides a 3D model of Trigonella foenum-graecum α-amylase and aids in understanding the atomic level molecular underpinnings of the mechanism of α-amylase interaction with substrate maltose. Ca²⁺ are essential for the stability of domain B since they are connected to it. Ca²⁺ site ligands are Asp¹³⁹, Glu¹³⁰, Thr¹³³, Asp¹³⁵ and Gly¹³¹ residues.

HIGHLIGHTS

• In silico analysis, gene prediction of α-amylase was carried from Trigonella foenum-graecum.

• Analysis of the structure of α-amylase was carried out using homology modelling.

• Calcium binding sites and their interactions with α-amylase were visualised using BIOVIA DISCOVERY STUDIO 2019.

• The molecular interaction between Trigonella foenum-graecum α-amylase and maltose was studied in silico using a molecular docking-based method.

• To give the required simulation parameters, RMSD, RMSF, and Total Energy were calculated using BIOVIA DISCOVERY STUDIO 2019.

Communicated by Ramaswamy H. Sarma

Keywords:

• α-Amylase
• Trigonella foenum-graecum
• homology modeling
• molecular docking
• molecular dynamics simulation
• calcium binding

Acknowledgements

We are thankful to School of Biotechnology and BTISNET Distributed Information Sub-Center, Centre of Bioinformatics, Institute of Science, Banaras Hindu University for the laboratory facilities. A.K. would like to thank Council of Scientific and Industrial Research (CSIR), New Delhi, for Junior and Senior Fellowships.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Funding

The author(s) reported there is no funding associated with the work featured in this article.